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bump version to v1.5.0
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@oschwengers
oschwengers committed Oct 5, 2020
1 parent 79aac56 commit de20930
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16 changes: 8 additions & 8 deletions README.md
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Expand Up @@ -85,7 +85,7 @@ All files are prefixed (`<prefix>`) as the input genome fasta file.
Platon can be installed in 2 different ways, though we advise to use Conda/BioConda.

In all cases, the custom database must be downloaded which we provide for download:
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3349651.svg)](https://doi.org/10.5281/zenodo.3349651)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4066768.svg)](https://doi.org/10.5281/zenodo.4066768)

### BioConda
1. install Platon via [Conda](https://conda.io/docs/install/quick.html) and the [Bioconda](https://bioconda.github.io/) channel
Expand All @@ -94,7 +94,7 @@ In all cases, the custom database must be downloaded which we provide for downlo
Example:
```
$ conda install -c conda-forge -c bioconda -c defaults platon
$ wget https://zenodo.org/record/3924529/files/db.tar.gz
$ wget https://zenodo.org/record/4066768/files/db.tar.gz
$ tar -xzf db.tar.gz
$ rm db.tar.gz
$ platon --db ./db genome.fasta
Expand All @@ -111,7 +111,7 @@ $ git clone git@github.com:oschwengers/platon.git
$ cd platon
$ python3 -m pip install .
$ cd ..
$ wget https://zenodo.org/record/3924529/files/db.tar.gz
$ wget https://zenodo.org/record/4066768/files/db.tar.gz
$ tar -xzf db.tar.gz
$ rm db.tar.gz
$ platon/bin/platon --db ./db genome.fasta
Expand Down Expand Up @@ -178,14 +178,14 @@ Platon provides 3 different modi controlling which filters will be used.
In the `sensitivity` mode Platon will classifiy all contigs with an `RDS` value *below*
the sensitivity threshold as chromosomal and all remaining contigs as plasmid.
This threshold was defined to account for 95% sensitivity and computed via Monte Carlo
simulations of artifical contigs resulting in an RDS=-7.7.
simulations of artifical contigs resulting in an RDS=-7.9.
-> use this mode to *exclude chromosomal* contigs.

### Specificity
In the `specificity` mode Platon will classifiy all contigs with an `RDS` value *above*
the specificity threshold as plasmid and all remaining contigs as chromosomal.
This threshold was defined to account for 99.9% specificity and computed via Monte Carlo
simulations of artifical contigs resulting in an RDS=0.4.
simulations of artifical contigs resulting in an RDS=0.7.

### Accuracy (default)
In the `accuracy` mode Platon will classifiy all contigs with:
Expand All @@ -204,9 +204,9 @@ Platon depends on a custom database based on MPS, RDS, RefSeq Plasmid database,
PlasmidFinder db as well as manually curated MOB HMM models from MOBscan,
custom conjugation and replication HMM models and oriT sequences from MOB-suite.
This database based on UniProt UniRef90 release 2020_01 can be downloaded here:
(zipped 1.4 Gb, unzipped 2.4 Gb)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3349651.svg)](https://doi.org/10.5281/zenodo.3349651)
- [https://zenodo.org/record/3924529/files/db.tar.gz](https://zenodo.org/record/3924529/files/db.tar.gz)
(zipped 1.6 Gb, unzipped 2.8 Gb)
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4066768.svg)](https://doi.org/10.5281/zenodo.4066768)
- [https://zenodo.org/record/4066768/files/db.tar.gz](https://zenodo.org/record/4066768/files/db.tar.gz)

## Dependencies
Platon was developed and tested in Python 3.5 and depends on BioPython (>=1.71).
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2 changes: 1 addition & 1 deletion platon/__init__.py
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__version__ = '1.4.0'
__version__ = '1.5.0'

9 comments on commit de20930

@Remigio1
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@Remigio1 Remigio1 commented on de20930 Oct 7, 2020 •
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ola quero muito usar o seu programa mas esta ocorrendo este erro:

platon --db ./db genome.fasta
ERROR: database file (rds.tsv) not readable!

meu python is: Python 3.5.5
my biopython is: 1.72
my platon version is 1.1.0
my system is: Linux lua 4.15.0-39-generic #42-Ubuntu SMP Tue Oct 23 15:48:01 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
database is https://zenodo.org/record/4066768/files/db.tar.gz

tambem ja tentei de outro computer:
mas o erro continua, abaixo está a configuracao do outro computador de onde tentei:
Python 3.8.3
Biopython 1.78
platon 1.1.0
my system: Linux x 5.3.0-59-generic #53~18.04.1-Ubuntu SMP Thu Jun 4 14:58:26 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
database is https://zenodo.org/record/4066768/files/db.tar.gz
por favor me ajude resolver este erro. quero muito testar o teu programa

@oschwengers
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Hello @Remigio1 , I'm very sorry but my ?Portugese? is not the best ;-) From some remaining Spanish skills I'd infer that you are using an outdated Platon version (v1.1) in combination with the latest db release (v1.5.). These two releases are not compatible.
Please, update Platon to the most recent release v1.5.0. Then, it should work again with yout db version.

Just in case the issues remain, please open a proper issue.
Best regards!

@Remigio1
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ola gracias por atenderme, para actualizar estoy usando el codigo
$ conda update platon
pero no actualiza, hay alguna otra forma de actualizar?
como puedo actualizar?
la version de mi bioconda es 4.8.4

@oschwengers
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Hola,
just try this:
$conda update platon=1.5.0

@Remigio1
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@Remigio1 Remigio1 commented on de20930 Oct 7, 2020 •
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Olá eu consegui atualizar da seguinte forma:
1 - baixei o arquivo noarch/platon-1.5.0-py_0.tar.bz2 no site: https://anaconda.org/bioconda/platon/files
2 - executei o comando conda install platon-1.5.0-py_0.tar.bz2
agora já estou com a versão 1.5.0
muito obrigado por ter me atendido, consegui resolver o problema.

@oschwengers
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nice to hear - you're welcome!

@Remigio1
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hello, I already updated the platon to version 1.5.0 but this is another error:
$ platon --db ./db genome.fasta
ERROR: genome file (/home/l/platon/genome.fasta) not readable!

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Olá, eu desistalei o platon e tentei instalar de outra forma mas esta dando erro:

$ git clone git@github.com:oschwengers/platon.git
Cloning into 'platon'...
The authenticity of host 'github.com (140.82.114.4)' can't be established.
RSA key fingerprint is SHA256:nThbg6kXUpJWGl7E1IGOCspRomTxdCARLviKw6E5SY8.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'github.com,140.82.114.4' (RSA) to the list of known hosts.
git@github.com: Permission denied (publickey).
fatal: Could not read from remote repository.

Please make sure you have the correct access rights
and the repository exists.

@oschwengers
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Hi, just try the https version oft the link;

git clone https://github.com/oschwengers/platon.git

Also, of course, you have to adopt the paths to both the db and the genome:

$ platon --db ./db genome.fasta

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